Contacts of the strand formed by residues 116 - 130 (chain A) in PDB entry 1SID
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 3.8 8.7 + - - -
111A ASP 4.5 1.4 - - - +
114A CYS* 2.8 20.5 + - - +
115A ASP* 1.3 85.6 + - - +
117A LEU* 1.3 63.5 + - - +
314A TRP* 3.5 31.8 - - + -
315A VAL 2.9 16.2 + - - +
19E CYS* 3.7 25.2 + - + +
20E PRO 3.7 18.5 + - - +
21E ARG* 4.6 5.0 + - - -
22E PRO* 4.6 9.1 - - + +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 3.5 29.4 - - + +
112A LEU* 4.4 6.7 - - + -
114A CYS 3.6 9.2 - - - +
116A THR* 1.3 81.0 - - - +
118A GLN* 1.3 64.7 + - - +
314A TRP* 3.1 9.1 - - - -
315A VAL* 2.9 37.7 + - + +
316A LYS 5.2 0.4 - - - +
317A ASN* 3.5 33.9 - - + +
318A PRO* 3.6 27.6 - - + -
319A TYR* 4.2 13.2 - - + -
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO* 4.1 10.6 - - - +
108A LEU* 3.6 40.9 + - + +
109A ASN* 4.1 14.9 + - - +
117A LEU* 1.3 79.3 - - - +
119A MET* 1.3 67.0 + - - +
276A GLU* 5.4 2.8 - - - +
312A LYS* 3.7 37.0 - - + +
313A ARG 3.3 15.5 - - - +
314A TRP* 3.4 40.2 + - + -
315A VAL* 4.6 1.8 - - - -
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 3.7 10.1 - - - -
118A GLN* 1.3 76.7 - - - +
120A TRP* 1.3 71.5 + - - +
121A GLU 3.4 0.2 + - - -
272A LEU* 3.9 33.4 - - + -
273A CYS 4.1 13.2 - - - +
274A LYS* 4.1 15.5 - - + -
276A GLU* 4.2 13.7 - - - +
312A LYS 3.7 0.7 - - - -
313A ARG* 2.7 44.8 + - + +
315A VAL* 3.8 30.5 - - + +
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Residues in contact with TRP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 5.4 4.7 - - + -
41A THR* 4.6 8.5 - - + -
45A SER* 4.9 2.0 - - - -
47A THR* 3.8 21.5 - - + -
105A LEU* 2.9 42.9 - - + +
106A PRO* 3.0 36.4 + - + +
108A LEU* 3.2 25.0 - - + +
119A MET* 1.3 77.3 - - - +
121A GLU* 1.3 59.6 + - - +
272A LEU* 3.2 5.5 - - - +
273A CYS* 2.8 47.8 + - + -
276A GLU* 4.2 13.1 + - + +
310A LEU* 3.4 23.1 - - + -
311A ARG* 3.6 11.7 - - - -
312A LYS* 3.7 35.0 - - + -
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TRP* 1.3 76.4 - - - +
122A ALA* 1.3 59.6 + - - +
123A VAL* 3.4 16.3 - - - +
264A LEU* 3.7 4.9 - - - +
269A VAL 2.9 27.4 - - - +
271A PRO 3.1 9.2 - - - +
272A LEU* 3.3 12.3 - - + -
273A CYS* 5.6 0.2 - - - -
310A LEU* 2.8 20.7 - - - +
311A ARG* 2.7 76.1 + - + +
313A ARG* 2.7 33.6 + - + -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A TRP 4.3 0.4 + - - -
121A GLU* 1.3 73.2 - - - +
123A VAL* 1.3 60.5 + - - +
167A VAL* 5.0 5.2 - - + -
263A LEU* 3.7 14.1 - - + -
264A LEU* 3.6 2.8 - - - +
270A GLY* 3.6 8.8 - - - -
271A PRO* 2.8 50.8 + - + +
273A CYS* 5.3 5.2 - - - -
278A LEU* 5.3 6.5 - - + -
308A ILE* 4.5 9.0 - - + -
310A LEU* 3.4 12.5 - - + +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.4 23.1 - - - +
122A ALA* 1.3 72.7 - - - +
124A SER* 1.3 73.3 + - - +
262A VAL* 3.2 7.3 - - + +
263A LEU* 2.7 24.7 + - - -
264A LEU* 3.2 21.4 + - + -
309A THR* 2.7 22.1 + - + +
310A LEU* 4.5 0.4 - - - -
311A ARG* 4.0 29.4 - - + +
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 1.3 94.6 - - - +
125A VAL* 1.3 67.0 + - - +
260A THR* 3.8 13.1 - - - +
261A THR 2.7 24.0 - - - -
262A VAL* 3.9 7.2 - - - -
263A LEU* 3.2 10.0 - - - +
308A ILE* 3.7 0.5 - - - -
309A THR* 3.0 37.5 + - - +
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A SER* 1.3 82.0 - - - +
126A LYS* 1.3 77.1 + - - +
127A THR* 3.8 13.9 + - + +
165A PHE* 5.0 4.7 - - + -
167A VAL* 4.6 10.8 - - + -
240A PHE* 6.1 0.7 - - + -
260A THR* 3.9 1.7 - - - +
261A THR* 2.5 38.7 + - - +
263A LEU* 3.0 31.4 - - + -
306A PHE* 4.5 8.1 - - + -
307A LYS 2.9 17.7 - - - +
308A ILE* 3.8 17.0 - - + -
309A THR* 4.2 1.6 - - - -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 1.3 82.0 - - - +
127A THR* 1.3 60.3 + - - +
256A THR 5.7 2.5 - - - +
257A ASN* 3.0 29.7 + - - +
258A THR* 3.5 12.0 + - - +
259A LEU 3.8 14.6 - - - +
260A THR* 3.3 36.1 - - + +
305A TYR* 4.5 9.0 - - + -
306A PHE* 3.5 0.2 - - - -
307A LYS* 2.8 65.1 + - + +
266B GLU* 3.7 24.6 + - - +
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.4 12.6 - - + +
126A LYS* 1.3 79.1 - - - +
128A GLU* 1.3 67.2 + - - +
165A PHE* 3.9 33.0 - - + -
256A THR 4.7 5.6 - - - +
259A LEU 4.6 4.8 + - - +
261A THR* 5.3 4.2 + - - +
304A ARG* 2.9 29.8 + - - +
305A TYR* 2.8 21.6 + - - -
306A PHE* 4.4 5.4 - - - -
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A THR* 1.3 83.0 + - - +
129A VAL* 1.3 73.0 + - - +
130A VAL* 3.7 13.0 + - + +
254A GLN 4.0 9.9 - - - +
255A PHE* 3.8 18.4 - - - -
256A THR 3.2 34.9 - - - +
257A ASN* 4.2 1.2 - - - -
304A ARG* 3.3 3.9 - - - +
305A TYR* 2.7 43.5 + - + +
229B PRO 4.2 2.1 - - - +
231B PRO* 3.9 12.9 - - + +
239B TYR* 2.8 32.1 + - - -
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLU* 1.3 78.4 - - - +
130A VAL* 1.3 64.3 + - - +
163A HIS* 5.1 3.4 - - + +
253A LEU* 3.0 43.4 - - + +
254A GLN 4.8 1.2 + - - +
255A PHE* 4.0 8.1 - - - -
284A ASP* 3.6 15.9 - - + +
286A MET* 5.4 0.7 - - - -
302A LEU* 3.6 27.1 - - + -
303A PRO 3.2 13.7 - - - +
304A ARG* 3.4 39.7 - - + +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLU* 3.9 27.1 - - - +
129A VAL* 1.3 78.0 - - - +
131A GLY* 1.3 62.2 + - - +
132A SER 3.7 0.9 - - - -
255A PHE* 4.1 5.4 - - + -
302A LEU* 3.3 9.0 - - - +
303A PRO* 3.1 50.8 + - + +
304A ARG* 4.7 1.3 - - - +
305A TYR* 4.9 3.4 - - + +
175B GLN* 6.2 2.0 - - + -
177B LEU* 3.9 9.3 - - + +
208B LEU* 4.7 11.7 - - + -
228B HIS* 4.8 5.6 - - + -
229B PRO 3.9 16.8 - - - +
230B ASP* 5.4 0.2 - - - -
231B PRO* 4.0 15.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il